0
votes
1
reply
1.3k
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 17 months ago by ★ 1.1k • written 17 months ago by • 0
0
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0
replies
588
views
EuroBioC2024 Flashtalks & Birds-of-a-Feather Sessions - submissions open!
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17 months ago Maria Doyle ▴ 110
0
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1
reply
755
views
Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData CEMiTool
updated 17 months ago by 68k • written 17 months ago by • 0
3
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3
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1.2k
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Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 17 months ago by 68k • written 17 months ago by ▴ 60
2
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3
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974
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updated 8 months ago by 16k • written 17 months ago by ★ 1.6k
0
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3
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1.7k
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makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
17 months ago Anna • 0
0
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3
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974
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 17 months ago by 68k • written 17 months ago by • 0
0
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4
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featureCounts error: Assertion `numOfBuckets > 0' failed
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18 months ago • updated 17 months ago Jessica • 0
2
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8
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4.1k
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biomaRt getLDS error
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17 months ago mark.dunning ▴ 20
1
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2
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945
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Question on number of genes used in GO analysis
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17 months ago Danté • 0
6
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15
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2.7k
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Deseq2 design formula and analysis with internal controls
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updated 17 months ago by ★ 1.4k • written 18 months ago by • 0
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4
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Failed to install geneLenDataBase
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updated 17 months ago by 4.3k • written 18 months ago by • 0
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4
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WTChimeraData() Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [experimenthub.bioconductor.org] Connection time-out
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18 months ago • updated 17 months ago haidan • 0
1
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2
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1.4k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
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18 months ago grothmn • 0
4
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4
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updated 17 months ago by ▴ 280 • written 18 months ago by • 0
1
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2
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mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
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18 months ago • updated 17 months ago Anke • 0
0
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8
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1.5k
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DiffBind full library size not reliable
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updated 17 months ago by ★ 5.2k • written 18 months ago by ▴ 20
1
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1
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1.1k
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biomaRt getSequence(): Error in .lock2
ensembldb getSequence
updated 18 months ago by ★ 6.6k • written 18 months ago by ▴ 10
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2
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save.rnb.set warnings when trying to save rnb.set
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5
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preprocessENmix colnames Error
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18 months ago • updated 17 months ago Eve • 0
0
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1
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1.4k
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
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updated 18 months ago by 68k • written 18 months ago by • 0
4
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7
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2.6k
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What does evidence of batch effect in bulk rnaseq look like?
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updated 17 months ago by ▴ 10 • written 19 months ago by ▴ 70
2
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4
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1.3k
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how limma work with continous variables
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0
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1
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932
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
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updated 18 months ago by 43k • written 18 months ago by • 0
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
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733
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18 months ago • updated 17 months ago Matthew Thornton ▴ 390
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7
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3
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2
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2
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3
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0
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944
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18 months ago shepherl 4.3k
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3
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updated 18 months ago by • 0 • written 2.4 years ago by • 0
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0
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624
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18 months ago louis.der.hammer • 0
0
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9
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'path' must be string
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updated 18 months ago by 68k • written 18 months ago by • 0
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4
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Recount3: PCR duplicates
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updated 18 months ago by ★ 5.0k • written 2.7 years ago by • 0
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6
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A question occur when using DESeq2 on a complex design
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3
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DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
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written 18 months ago by ▴ 10
0
votes
0
replies
723
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Error in serialization
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18 months ago Lluís Revilla Sancho ▴ 760
0
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1
reply
770
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Retrieving Package Metadata from Bioconductor API: Versions and Dependencies
metaMSdata
updated 18 months ago by 4.3k • written 18 months ago by • 0
4
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12
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How to get DMR for Infinium methylation EPIC v2
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updated 18 months ago by ▴ 230 • written 2.2 years ago by ▴ 20
0
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3
replies
1.0k
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
18 months ago gallantk5 • 0
0
votes
3
replies
1.1k
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
1
vote
1
reply
1.2k
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Why does greyListChIP return different grey lists every time I newly run the script?
GreyListChIP
updated 18 months ago by ▴ 10 • written 18 months ago by • 0
0
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0
replies
723
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
18 months ago ramiro.barrantes ▴ 10
0
votes
8
replies
1.9k
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Error running tximeta
tximeta
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
0
votes
4
replies
1.6k
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Generating surrogate variables across multiple variables of interest
sva
18 months ago Robert • 0
1
vote
6
replies
1.4k
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limma and Syntactically Invalid Factor Values
limma
updated 18 months ago by 53k • written 18 months ago by ★ 1.6k
1
vote
1
reply
1.1k
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
18 months ago Bioinformagician • 0
1
vote
3
replies
980
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Doubt about model in paired samples (intercept ?)
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
0
votes
10
replies
2.2k
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Two treatments, one control
DESeq2 stageR
18 months ago alephreish • 0
1,000 results • Page 19 of 20
Recent ...
Replies
Answer: lfc shrinkage estimator in DESeq2 by plumsgorillas • 0
You are on the right track. In DESeq2, raw log2 fold changes are often noisy and can be misleading, especially for genes with low counts. A…
Answer: Array weights in dpcDE by Gordon Smyth 53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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